The first description of the complete genome sequence of multidrug-resistant Salmonella enterica serovar monophasic Typhimurium (1,4,[5],12:i:-) isolate with the mcr-1.1 gene on IncHI2 found in pig in Poland

Monophasic Salmonella Typhimurium (1,4,[5],12:i:-) is one of the leading Salmonella serovars causing human salmonellosis in Europe. It has been observed in Poland since 2008. This serovar is considered the one with the highest rate of mcr prevalence. This report presents a sequence characteristic of the multidrug-resistant (MDR) monophasic S. Typhimurium isolated from a pig faecal sample with the confirmed presence of the mcr-1.1 gene. The genome was assembled into the complete chromosome and 4 plasmids: IncHI2 (232 119 bp), IncFIB/IncFIC (133 901 bp), ColRNAI (6659 bp), and Col8282 (4066bp). The strain identified as ST34 carried multiple antimicrobial resistance genes located both on chromosome (tet(B)) and plasmids: mcr-1.1 and blaTEM-1B on ST4-IncHI2, and mef(B), blaTEM-1B, aadA1, qacL, dfrA12, aadA2, cmlA1, sul3, tet(M) on IncFIB/FIC. The mcr-1.1 gene was previously identified in E. coli deriving mainly from poultry, but this is the first case of the occurrence of mcr-positive Salmonella in Poland. The obtained results of analysis of the genome content draw attention to the problem of multidrug-resistant pathogens, especially in the context of resistance to colistin which is a last-resort antimicrobial.

Cryptic SARS-CoV-2 lineage identified on two mink farms as a possible result of long-term undetected circulation in an unknown animal reservoir, Poland, November 2022 to January 2023

In late 2022 and early 2023, SARS-CoV-2 infections were detected on three mink farms in Poland situated within a few km from each other. Whole-genome sequencing of the viruses on two of the farms showed that they were related to a virus identified in humans in the same region 2 years before (B.1.1.307 lineage). Many mutations were found, including in the S protein typical of adaptations to the mink host. The origin of the virus remains to be determined.

Attempting to Identify Bacterial Allies in Immunotherapy of NSCLC Patients

Introduction: Factors other than PD-L1 (Programmed Death Ligand 1) are being sought as predictors for cancer immuno- or chemoimmunotherapy in ongoing studies and long-term observations. Despite high PD-L1 expression on tumor cells, some patients do not benefit from immunotherapy, while others, without the expression of this molecule, respond to immunotherapy. Attention has been paid to the composition of the gut microbiome as a potential predictive factor for immunotherapy effectiveness. Materials and Methods: Our study enrolled 47 Caucasian patients with stage IIIB or IV non-small cell lung cancer (NSCLC). They were eligible for treatment with first- or second-line immunotherapy or chemoimmunotherapy. We collected stool samples before the administration of immunotherapy. We performed next-generation sequencing (NGS) on DNA isolated from the stool sample and analyzed bacterial V3 and V4 of the 16S rRNA gene. Results: We found that bacteria from the families Barnesiellaceae, Ruminococcaceae, Tannerellaceae, and Clostridiaceae could modulate immunotherapy effectiveness. A high abundance of Bacteroidaaceae, Barnesiellaceae, and Tannerellaceae could extend progression-free survival (PFS). Moreover, the risk of death was significantly higher in patients with a high content of Ruminococcaceae family (HR = 6.3, 95% CI: 2.6 to 15.3, p < 0.0001) and in patients with a low abundance of Clostridia UCG-014 (HR = 3.8, 95% CI: 1.5 to 9.8, p = 0.005) regardless of the immunotherapy line. Conclusions: The Clostridia class in gut microbiota could affect the effectiveness of immunotherapy, as well as the length of survival of NSCLC patients who received this method of treatment.

Presence of Akkermansiaceae in gut microbiome and immunotherapy effectiveness in patients with advanced non-small cell lung cancer

The significance of Akkermansia bacteria presence in gut micobiome, mainly Akkermansia mucinifila, is currently being investigated in the context of supporting therapy and marker for response to immunotherapy in cancer patients. It is indicated that patients with non-small cell lung cancer (NSCLC) treated with immune checkpoint inhibitors (ICIs) respond better to treatment if this bacterium is present in the intestine.

We performed next-generation sequencing of the gut microbiome from patients treated in the first or second line therapy with anti-PD-1 (anti-programmed death 1) or anti-PD-L1 (anti-programmed death ligand 1) monoclonal antibodies. In our study group of 47 NSCLC patients, the percentage of Akkermansiaceae was higher in patients with disease stabilization and with partial response to immunotherapy compared to patients with disease progression. Moreover, we found that a higher percentage of Akkermansiaceae was present in patients with squamous cell carcinoma compared to adenocarcinoma. Our study showed that Akkermansiaceae could be supporting marker for response to immunotherapies in NSCLC patients, nonetheless further in-depth studies should be conducted in the role of Akkermansiaceae in cancer immunotherapy.

Composition of the microbiome can influence patients response to immunotherapy

Response to immunotherapy of NSCLC patients is associated with the presence of Akkermansiaceae in the gut

Akkermansia could be used as a predictor for patient treated with immunological checkpoint inhibitors

Whole-genome sequence analysis of Salmonella Infantis isolated from raw chicken meat samples and insights into pESI-like megaplasmid

There has been an increase in the number of reports on Salmonella enterica subsp. enterica serovar Infantis (S. Infantis) isolated from animals and humans. Recent studies using whole genome sequencing (WGS) have provided evidence on the likely contribution of a unique conjugative megaplasmid (pESI; ~280 kb) to the dissemination of this serovar worldwide. In the present study, twenty-two unrelated Salmonella strains [S. Infantis (n = 20) and Salmonella 6,7:r:- (n = 2)] and their plasmids were investigated using next generation sequencing technologies (MiSeq and MinION) to unravel the significant expansion of this bacteria in Turkey. Multi-locus sequence typing, plasmid replicons, resistance gene contents as well as phylogenetic relations between strains were determined. According to the WGS data, all S. Infantis possessed the relevant megaplasmid backbone genes and belonged to sequence type 32 (ST32) with the exception of a single novel ST7091. Tetracycline and trimethoprim/sulfamethoxazole resistance were found to be widespread in S. Infantis strains and the resistant strains exclusively carried the tetA, sul1, sul2 and dfrA14 genes. One S. Infantis isolate was also a carrier of the plasmid-mediated ampC via bla_CMY-2, gene. Moreover, full genomes of four S. Infantis isolates were reconstructed based on hybrid assembly. All four strains contained large plasmids (240-290 kb) similar to previously published megaplasmid (pESI) and accompanied by several small plasmids. The megaplasmid backbone contained a toxin-antitoxin system, two virulence cassettes and segments associated with heavy metals resistance, while variable regions possessed several antibiotic resistance genes flanked by mobile elements. This study indicated that pESI-like megaplasmid is widely disseminated within the tested S. Infantis strains of chicken meat, warranting further genomic studies on clinical strains from humans and animals to uncover the overall emergence and spread of this serovar.

A Turkey-origin H9N2 Avian Influenza Virus Shows Low Pathogenicity but Different Within-Host Diversity in Experimentally Infected Turkeys, Quail and Ducks

Avian influenza virus (AIV) is a highly diverse and widespread poultry pathogen. Its evolution and adaptation may be affected by multiple host and ecological factors, which are still poorly understood. In the present study, a turkey-origin H9N2 AIV was used as a model to investigate the within-host diversity of the virus in turkeys, quail and ducks in conjunction with the clinical course, shedding and seroconversion. Ten birds were inoculated oculonasally with a dose of 10⁶ EID₅₀ of the virus and monitored for 14 days. Virus shedding, transmission and seroconversion were evaluated, and swabs collected at selected time-points were characterized in deep sequencing to assess virus diversity. In general, the virus showed low pathogenicity for the examined bird species, but differences in shedding patterns, seroconversion and clinical outcome were noted. The highest heterogeneity of the virus population as measured by the number of single nucleotide polymorphisms and Shannon entropy was found in oropharyngeal swabs from quail, followed by turkeys and ducks. This suggests a strong bottleneck was imposed on the virus during replication in ducks, which can be explained by its poor adaptation and stronger selection pressure in waterfowl. The high within-host virus diversity in quail with high level of respiratory shedding and asymptomatic course of infection may contribute to our understanding of the role of quail as an intermediate host for adaptation of AIV to other species of poultry. In contrast, low virus complexity was observed in cloacal swabs, mainly from turkeys, showing that the within-host diversity may vary between different replication sites. Consequences of these observations on the virus evolution and adaptation require further investigation.

Determination of telomere length and telomerase activity in cattle infected with bovine leukaemia virus (BLV)

Telomeres are repetitive sequence structures at the ends of chromosomes. They consist of the double stranded DNA repeats followed by the short single stranded DNA. In humans and other verterbrates the telomeric sequence is composed of tandem of TTAGGG repeats. With each cells division telomeres shorten by up to 200 base pairs. Telomerase is an enzyme responsible for continuous cell growth and is repressed in most somatic cells, except proliferating progenitor cells, but in more than 85% of cancer cells telomerase expression is observed. Tumour cells with metastatic potential may demonstrate a high telomerase activity, allowing cells to escape from the inhibition of cell proliferation due to shortened telomeres. Determination of telomerase expression was performed with the use of PCR ELISA in samples isolated from bovine leukaemia virus (BLV) infected cows. Telomerase activity was found in almost all investigated samples. The relative telomerase activity (RTA) was higher in infected cows than in healthy animals and the differences were statistically significant (α=0.05). In blood lymphocytes of BLV-infected cows the mean values of telomerase expression determined in real-time PCR were 3534.12 copies, in the healthy group there were 1010.10 copies and these differences were also statistically significant. For telomere length evaluation the Telomere PNA/FITC FISH and Telomere PNA/FITC FISH for flow cytometry were used. The mean fluorescence intensity of telomere sequences calculated on the surface of interphase nuclei of leukaemic blood lymphocytes was lower than that in the control animals and the difference was statistically significant. The mean length of telomeres in BLV- infected and healthy cows was 31.63 ± 12.62 and 38.4 ± 4.03, (p=0.112), respectively.

Evaluation of Direct Metagenomics and Target Enriched Approaches for High-throughput Sequencing of Field Rabies Viruses

INTRODUCTION

High-throughput sequencing (HTS) identifies random viral fragments in environmental samples metagenomically. High reliability gains it broad application in virus evolution, host-virus interaction, and pathogenicity studies. Deep sequencing of field samples with content of host genetic material and bacteria often produces insufficient data for metagenomics and must be preceded by target enrichment. The main goal of the study was the evaluation of HTS for complete genome sequencing of field-case rabies viruses (RABVs).

MATERIAL AND METHODS

The material was 23 RABVs isolated mainly from red foxes and one European bat lyssavirus-1 isolate propagated in neuroblastoma cells. Three methods of RNA isolation were tested for the direct metagenomics and RABV-enriched approaches. Deep sequencing was performed with a MiSeq sequencer (Illumina) and reagent v3 kit. Bioinformatics data were evaluated by Kraken and Centrifuge software and de novo assembly was done with metaSPAdes.

RESULTS

Testing RNA extraction procedures revealed the deep sequencing scope superiority of the combined TRIzol/column method. This HTS methodology made it possible to obtain complete genomes of all the RABV isolates collected in the field. Significantly greater rates of RABV genome coverages (over 5,900) were obtained with RABV enrichment. Direct metagenomic studies sequenced the full length of 6 out of 16 RABV isolates with a medium coverage between 1 and 71.

CONCLUSION

Direct metagenomics gives the most realistic illustration of the field sample microbiome, but with low coverage. For deep characterisation of viruses, e.g. for spatial and temporal phylogeography during outbreaks, target enrichment is recommended as it covers sequences much more completely.

Determination of cytokine profiles in populations of dendritic cells from cattle infected with bovine leukaemia virus

Dendritic cells (DCs) due to their ability to present antigens are essential during the immune response to infections. The aim of the study was to evaluate the influence of bovine leukaemia virus (BLV) infection on DC properties. Cytokine profiles of myeloid, plasmacytoid and mono- cyte derived DCs from BLV infected cattle were analysed. Concentrations of IL-6, IL-10, IL-12, IFN-γ, and TNF-α in DC cultures were measured by flow cytometry. Obtained results indicated activation of pDCs population, where a significant increase in production of the IFN-γ was shown. Meanwhile, a decrease in production of IFN-γ and increase in production of IL-10 were shown in mDCs; the main population responsible for antigens presentation. This may indicate a contribu- tory role of the population during the process of persistent infection. In MoDCs population a significant elevation in secretion of proinflammatory cytokines - IL-6 and TNF-α was noted.

Cytokine profiles of dendritic cells (DCs) during infection with bovine leukaemia virus (BLV)

BLV is an agent of enzootic bovine leukaemia (EBL), an infectious disease affecting cattle worldwide. BLV infection has been associated with immune system disorders and discrepancies in the cytokine network. The significance of dendritic cells in the pathogenesis of BLV infection is largely unknown, but considering their fundamental role in immune response it may be crucial. DCs precursors were isolated with the use of immunomagnetic beads from BLV-infected and BLV-free cows. From these precursors cultures of monocyte derived dendritic cells (MoDCs) were generated with the use of a cytokine cocktail (IL-4 and GM-CSF). Additionally, parallel DCs from BLV-negative animals were infected in vitro. The level of cytokines: IL-6, IL-10, IL-12(p40), IL-12(p70) was determined in DC cultures: infected in vitro, originating from naturally infected cattle and BLV-free cattle. The investigation showed significant changes in almost all analyzed populations of BLV-infected DCs. Cytokine profiles of blood MoDCs indicated activation of these groups during infection. In the case of spleen MoDCs and lymph node MoDCs a decrease in production of IL-12(p40) and IL-12(p70) in favour of IL-6 and IL-10 was noted, suggesting promotion of BLV infection development.

[Neurofeedback therapy influence on clinical status and some EEG parameters in children with localized epilepsy]

Neurofeedback (EEG biofeedback, NF) is one of the methods of non-pharmacological instrumental therapy. In the treatment of epilepsy it is considered as a complementary method, reducing the number of seizures. The aim of this study was to investigate the effect of NF on the incidence of clinical attacks and bioelectrical activity of the brain in children with epilepsy with partial seizures and secondarily generalized seizures.

MATERIAL AND METHODS

The study involved a group of 78 children with partial seizures, additionally 30 of them had second-ry generalized seizures. There were 35 girls and 43 boys ranging in age from 5 to 17.5 years. They were treated with NF in the Neuromedica Institute in Krakow, in the period 2005-2015. Treatment time ranged from 6 months to 3 years. We have evaluated the incidence of seizures before and after NF therapy. Visual analysis of EEG recordings with assessment of background activity, location of focal changes, presence of paroxysmal pattern and epileptic graphoelements.

RESULTS

In 41/78 children seizures occurred 1-2 times a month, in 19/78 every day and 9 children were diagnosed with epileptic syndrome. During NF therapy 52/78 children experienced resolution of clinical seizures. NF therapy was ineffective in only one child. In 18 child withdrawal of antiepileptic treatment was achieved and in 22 reduction of drug doses. Epileptic graphoelements occurred in 46/78 children before treatment and in 21/78 children after treatment. Before NF therapy irregular bio-electrical activity was found in 51 children versus 27 children with regular bioelectric activity and in 27 children versus 51 children after the therapy. The amplitude of this activity returned to normal in 19 children, and in 29 children the frequency of background activity. Particularly surprising was to restore synchrony and symmetry of EEG pattern in 44 children (11 children before NF treatment to 55 children after the treatment). Even more significant effect of NF therapy was observed in EEG patterns, abolition of paroxysmal pattern and reduction of continuous, localized and generalized changes. NF therapy also advantageously reduced the number of localized changes and decreased sensitivity of EEG pattern to hyperventilation and photostimulation.

CONCLUSIONS

During NF therapy in almost all children with epileptic partial seizures and secondarily generalized seizures resolution or reduction of clinical seizures was observed. In nearly 1/4 of children withdrawal of antiepileptic treatment was achieved and in higher number reduction of pharmacotherapy. All parameters of the background EEG bioelectric activity in these children have improved, especially synchrony and symmetry of EEG pattern and paroxysmal changes subsided.